Figure 1. Prospective validation using hitherto uncharacterized HLA molecules.
The upper figure gives the IC50 binding values for the sets of peptides identified by the NetMHCpan method to bind two hitherto uncharacterized HLA-A*8001, and HLA-A*7401 molecules. The peptides were selected as described in the text. 86% of the tested peptides bind stronger than 500 nM. The lower figure shows a Kullback-Leibler [52] logo visualization of the HLA binding motifs as predicted by the NetMHCpan method. Peptide binders used to generate the logos for each HLA molecule were selected from a pool of 500,000 random natural nonamers using the NetMHCpan method with a binding threshold of 500 nM. The logos were generated with the logo program of Schneider and Stephens [53]. Note that the binding motifs visualized in the logo plot are estimated from a set of approximately 5000 predicted binders, whereas the validated peptides only make up of the top 0.2%.